Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.

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Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies

Bacterial communities are important for the health and productivity of soil ecosystems, and have great potential as novel indicators of environmental perturbations To assess how they are affected by anthropogenic activity, and determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses We determined, through 16S rRNA amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart Overall, soil bacterial communities varied more in response to changing soil environments than changes in climate or increasing geographic distance We identified strong correlations between the relative abundance of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon to nitrogen ratio, Bradyrhizobium and the levels of Olsen P, and members of Chitinophagaceae and aluminium concentrations These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms, but also demonstrates the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even when comparing samples across large geographic areas and diverse soil types Overall, we provide strong evidence that there is scope to use relative taxa abundances as biological indicators of soil condition Importance The impact of land use change and management on soil microbial community composition remains poorly understood Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition We included variables related to anthropogenic activity, and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales, soil, and land use types Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil, and thereby influence the way we monitor the effects of anthropogenic activity on soil ecosystems into the future

Bacteria as Emerging Indicators of Soil Condition

Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation

The availability of carbon (C) from high levels of atmospheric carbon dioxide (CO2) and anthropogenic release of nitrogen (N) is increasing, but these increases are not paralleled by increases in levels of phosphorus (P). The current unstoppable changes in the stoichiometries of C and N relative to P have no historical precedent. We describe changes in P and N fluxes over the last five decades that have led to asymmetrical increases in P and N inputs to the biosphere. We identified widespread and rapid changes in N:P ratios in air, soil, water, and organisms and important consequences to the structure, function, and biodiversity of ecosystems. A mass-balance approach found that the combined limited availability of P and N was likely to reduce C storage by natural ecosystems during the remainder of the 21st Century, and projected crop yields of the Millennium Ecosystem Assessment indicated an increase in nutrient deficiency in developing regions if access to P fertilizer is limited. Imbalances of the N:P ratio would likely negatively affect human health, food security, and global economic and geopolitical stability, with feedbacks and synergistic effects on drivers of global environmental change, such as increasing levels of CO2, climatic warming, and increasing pollution. We summarize potential solutions for avoiding the negative impacts of global imbalances of N:P ratios on the environment, biodiversity, climate change, food security, and human health.

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Anthropogenic global shifts in biospheric N and P concentrations and ratios and their impacts on biodiversity, ecosystem productivity, food security, and human health.

Responses of soil microbial communities and their network interactions to saline-alkaline stress in Cd-contaminated soils.

Long-term effects of imbalanced fertilization on the composition and diversity of soil bacterial community

Effects of dazomet on soil organisms and recolonisation of fumigated soil

Effects of manure composts on soil biota and root-rot disease incidence of ginseng (Panax ginseng)

This study investigated the effects of rice husk and rice husk biochar on root rot (caused by Cylindrocarpon destructans and Fusarium solani) of ginseng (Panax ginseng) and on soil organisms. The effects were compared between paddy-converted and upland soils characterised by high and low nutrient content, respectively. The prevalence of root rot disease in the upland soil decreased in plots treated with rice husk at 5.2 Mg ha−1 compared to the untreated control. Small differences in soil chemical properties between different treatments suggested the role of biotic factors in the suppression of the disease. In both soils, the lowest hyphal growth of Fusarium solani was observed in soil collected from plots treated with rice husk at 5.2 Mg ha−1. The results suggested that the low incidence of root rot disease was due to the suppressive effect of soil on pathogenic fungi in the treated upland soil. Principal component analysis of phospholipid fatty acid results suggested that changes in microbial com...

Effects of rice husk and rice husk biochar on root rot disease of ginseng (Panax ginseng) and on soil organisms

Plant-specific effects of sunn hemp (Crotalaria juncea) and sudex (Sorghum bicolor × Sorghum bicolor var. sudanense) on the abundance and composition of soil microbial community

Kee-Choon Park

Papers

Long-term effects of imbalanced fertilization on the composition and diversity of soil bacterial community

Effects of dazomet on soil organisms and recolonisation of fumigated soil

Effects of manure composts on soil biota and root-rot disease incidence of ginseng (Panax ginseng)

Effects of rice husk and rice husk biochar on root rot disease of ginseng (Panax ginseng) and on soil organisms

Plant-specific effects of sunn hemp (Crotalaria juncea) and sudex (Sorghum bicolor × Sorghum bicolor var. sudanense) on the abundance and composition of soil microbial community